Merge branch 'release-0.1.0'

.dockerignore

@@ -0,0 +1,5 @@
+/**
+!/CMakeLists.txt
+!/src
+!/thirdparty
+!/docker

.github/workflows/bump-homebrew-formula.yml

@@ -0,0 +1,29 @@
+name: Bump Homebrew formula
+
+on:
+  release:
+    types: [ published ]
+
+jobs:
+  homebrew:
+    name: Bump Homebrew formula
+    runs-on: ubuntu-latest
+    steps:
+      - name: Get the version
+        id: get_version
+        run: echo ::set-output name=VERSION::${GITHUB_REF/refs\/tags\//}
+
+      - name: Update homebrew tap
+        uses: mislav/[email protected]
+        with:
+          formula-name: city4cfd
+          formula-path: Formula/city4cfd.rb
+          homebrew-tap: tudelft3d/homebrew-software
+          base-branch: main
+          download-url: https://github.com/tudelft3d/city4cfd/archive/${{ steps.get_version.outputs.VERSION }}.tar.gz
+          commit-message: |
+           Bumped {{formulaName}} to {{version}}
+
+            Created by https://github.com/mislav/bump-homebrew-formula-action
+        env:
+          COMMITTER_TOKEN: ${{ secrets.COMMITTER_TOKEN }}

.gitignore

@@ -8,4 +8,5 @@ Mesh*.json
 *.stl
 *.swp
 *.log
-thirdparty/LAStools/bin64
+thirdparty/LAStools/bin64/*
+!/thirdparty/LAStools/bin64/serf

CHANGELOG.md

@@ -0,0 +1,4 @@
+# Changelog
+
+## [0.1.0] - 2022-08-14 
+First release

CITATION.bib

@@ -0,0 +1,9 @@
+@article{Paden2022,
+  author={Paden, Ivan, Garc{\'i}a-S{\'a}nchez Clara and Ledoux, Hugo},   
+  title={Towards Automatic Reconstruction of 3D City Models Tailored for Urban Flow Simulations},      	
+  journal={Frontiers in Built Environment},      
+  volume={8},           
+  year={2022},            	
+  doi={10.3389/fbuil.2022.899332},
+  ISSN={2297-3362},   
+}

CMakeLists.txt

@@ -1,39 +1,67 @@
 cmake_minimum_required(VERSION 3.1)
 
-project(City4CFD)
+project(city4cfd)
 
 #set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake/Modules/" ${CMAKE_MODULE_PATH})
 #set( CMAKE_ALLOW_LOOSE_LOOP_CONSTRUCTS true )
 
-set( CMAKE_CXX_FLAGS "-O3" )
-set( CMAKE_BUILD_TYPE "Release" )
-#set( CMAKE_BUILD_TYPE "Debug" )
+set(CMAKE_CXX_FLAGS "-O3")
+set(CMAKE_BUILD_TYPE "Release")
+#set(CMAKE_BUILD_TYPE "Debug")
 
-#if ( COMMAND cmake_policy )
-#    cmake_policy( SET CMP0003 NEW )
+#if (COMMAND cmake_policy)
+#    cmake_policy(SET CMP0003 NEW)
 #endif()
 
+#==============================
+# Alpha wrap support
+set(ALPHA_WRAP_SUPPORT OFF)
+#==============================
+
 # BOOST
-find_package( Boost REQUIRED COMPONENTS filesystem)
+find_package(Boost 1.66 REQUIRED COMPONENTS filesystem)
 
 # CGAL
-find_package( CGAL REQUIRED QUIET COMPONENTS)
-
-# LAStools
-add_subdirectory(  ${CMAKE_SOURCE_DIR}/thirdparty/LAStools )
+find_package(CGAL REQUIRED QUIET COMPONENTS)
+if (CGAL_FOUND)
+    if (CGAL_VERSION VERSION_GREATER_EQUAL "5.3")
+        message(STATUS "Found CGAL ${CGAL_VERSION}")
+    elseif (CGAL_VERSION VERSION_GREATER_EQUAL "5.0")
+        message(STATUS "Found CGAL version greater than 5.0, but less than 5.3. "
+                "Proceeding to compile with included CGAL headers.")
+        include_directories(${CMAKE_SOURCE_DIR}/thirdparty/CGAL/include)
+        set(CGAL_USE_INCLUDED_HEADERS ON)
+    else()
+        message(FATAL_ERROR "Found CGAL version ${CGAL_VERSION} which is not supported!"
+                "Please use CGAL version 5")
+        return()
+    endif ()
+endif ()
+if (NOT CGAL_USE_INCLUDED_HEADERS AND ALPHA_WRAP_SUPPORT)
+    message(STATUS "Requested alpha wrap support. Compiling with included CGAL headers.")
+    include_directories( ${CMAKE_SOURCE_DIR}/thirdparty/CGAL/include )
+endif()
 
 # Third-party
-include_directories( ${CMAKE_SOURCE_DIR}/thirdparty )
-include_directories( ${CMAKE_SOURCE_DIR}/thirdparty/valijson )
+add_subdirectory(${CMAKE_SOURCE_DIR}/thirdparty/LAStools)
+include_directories(${CMAKE_SOURCE_DIR}/thirdparty)
+include_directories(${CMAKE_SOURCE_DIR}/thirdparty/valijson)
+include_directories(${Boost_INCLUDE_DIR})
 
 # Creating entries for target: City4CFD
 FILE(GLOB SRC_FILES "src/*.cpp")
-add_executable(City4CFD ${SRC_FILES})
+add_executable(city4cfd ${SRC_FILES})
 set_target_properties(
-        City4CFD
+        city4cfd
         PROPERTIES CXX_STANDARD 14
 )
 
-target_link_libraries( City4CFD ${CGAL_LIBRARIES} ${CGAL_3RD_PARTY_LIBRARIES} Boost::filesystem)
+target_link_libraries(city4cfd
+        ${CGAL_LIBRARIES}
+        ${CGAL_3RD_PARTY_LIBRARIES}
+        ${Boost_SYSTEM_LIBRARY}
+        ${Boost_FILESYSTEM_LIBRARY}
+        LASlib
+        )
 
-install(TARGETS City4CFD DESTINATION bin)
+install(TARGETS city4cfd DESTINATION bin)

README.md

@@ -1 +1,96 @@
+[![docs](https://img.shields.io/badge/docs-Wiki-brightgreen)](https://github.com/tudelft3d/City4CFD/wiki)
+[![GitHub license](https://img.shields.io/github/license/tudelft3d/City4CFD)](https://github.com/tudelft3d/City4CFD/blob/master/LICENSE)
+[![DOI:10.3389/fbuil.2022.899332](http://img.shields.io/badge/DOI-10.3389/fbuil.2022.899332-B62030.svg)](https://www.frontiersin.org/articles/10.3389/fbuil.2022.899332)
+
+
 # City4CFD
+
+![welcome_figure](https://github.com/tudelft3d/City4CFD/blob/main/docs/images/workflow.png)
+
+City4CFD--*City for CFD*--is a tool that aims to automatically reconstruct 3D city geometries tailored for microscale urban flow simulations.
+
+It can create automatically a terrain from a point cloud and imprint different surfaces (e.g. green areas, water, roads).
+
+It enables us to reconstruct buildings from different sources and their combination, such as:
+  - Reconstruction with the combination of 2D polygons and a point cloud,
+  - Extrusion of footprints containing height or floor number attributes,
+  - The import of existing building models.
+
+The resulting geometry is watertight -- buildings and surfaces are seamlessly integrated into a terrain.
+
+It can automatically or manually define the zone of influence and domain boundaries.
+
+If you happen to use it, feedback is very much appreciated.
+
+City4CFD is developed by the [3D Geoinformation Research Group](https://3d.bk.tudelft.nl/) at the Delft University of Technology.
+
+## Data formats
+**Point clouds** can be imported in LAS/LAZ, XYZ, or PLY format. We ask separately for ground and building points. While some datasets contain building-ground classification, some do not. In case your LAS/LAZ file has buildings/ground classified, you can use [point cloud preparation script](https://github.com/tudelft3d/City4CFD/blob/main/tools/prepare_point_cloud.sh) to create separate files. If buildings and terrain are under the same class, or vegetation is not filtered out, we suggest you use [CloudCompare](https://www.danielgm.net/cc/) to prepare points.
+
+**2D data** (polygons) are imported in GeoJSON format. For all pre-processing related to polygons, including conversion to GeoJSON, you can use [QGIS](https://qgis.org/en/site/).
+
+**Geometry import** supports the following formats: OBJ, STL, PLY, OFF, VTP, and CityJSON.
+
+**Output** is in the following formats: OBJ, STL, and CityJSON. The ID of each polygon is preserved, and there is a 1-to-1 mapping between the input and the output.
+
+## Installation
+You can directly compile City4CFD on your system using cmake, run it through a Docker container, or install using Homebrew in case of macOS.
+
+### Build from source
+The following libraries are required to build the project:
+- [CGAL](https://www.cgal.org/) version 5
+- Boost >= 1.66
+
+Both dependencies are generally available in Linux distributions (Debian/Ubuntu/Mint) as *libcgal-dev* and *libboost-dev*, and in macOS with Homebrew as *cgal* and *boost*.
+The project uses CMake to generate makefiles, so make sure it is also installed.
+
+To build City4CFD, do the following:
+```
+mkdir build && cd build
+cmake ..
+make
+./city4cfd
+```
+You can speed up compilation by typing *make -j $numcores* where *$numcores* is the number of threads you can spare for compilation.
+
+### Docker
+We offer built [Docker](https://www.docker.com/) images for every release, available at the [Docker Hub](https://hub.docker.com/r/tudelft3d/city4cfd). Running the docker script for the first time will pull the docker image from the Docker Hub repository.
+
+### macOS
+Mac users can install City4CFD through Homebrew:
+
+```
+brew tap tudelft3d/software
+brew install city4cfd
+```
+
+## Getting started
+
+The folder *examples* contains example datasets you can run for your first reconstruction. You can run your first reconstruction from the `/examples/TUD_Campus` folder by typing:
+```
+mkdir results
+../../build/city4cfd config_bpg.json --output_dir results
+```
+in case of building from a source.
+
+To run through a Docker container, you can use one of the scripts in ```docker/run/```. The script with the extension ```.sh``` can be used in Linux and macOS, the one with the extension ```.ps1``` in Windows Powershell, and the last one with ```.bat``` in Windows Command Prompt. You have to run  a script (you can copy it beforehand) from the root directory of the project (e.g. ```examples/TUD_Campus```), and the arguments are the same as for the compiled executable, e.g.: 
+
+```
+../../docker/run/city4cfd_run.sh config_bpg.json --output_dir results
+```
+
+The script pulls the ```latest``` release from the Docker Hub. For a specific release, replace ```latest``` in the script with the released version tag, e.g. ```0.1.0```. In Linux systems, you will probably have to run the command as a sudo unless you create a 'docker' group and add users to it.
+
+More information on the project can be found in the documentation.
+
+## Documentation
+The [wiki section](https://github.com/tudelft3d/City4CFD/wiki) of this project has details on reconstruction setup and also contains information and suggestions on data preparation.
+
+## Citation
+If you use City4CFD in a scientific context, please cite the following paper:
+
+Pađen, Ivan, García-Sánchez, Clara and Ledoux, Hugo (2022). Towards Automatic Reconstruction of 3D City Models Tailored for Urban Flow Simulations. *Frontiers in Built Environment*, 8, 2022 [[DOI](https://www.frontiersin.org/articles/10.3389/fbuil.2022.899332)][[BibTeX](https://github.com/tudelft3d/City4CFD/blob/master/CITATION.bib)]
+
+## Acknowledgements
+We would like to acknowdledge the authors of supporting libraries we use in this project:
+[CGAL](https://github.com/CGAL/cgal), [nlohmann/json](https://github.com/nlohmann/json), [valijson](https://github.com/tristanpenman/valijson), [LAStools](https://github.com/LAStools)

docker/build-base.sh

@@ -0,0 +1 @@
+docker build -f city4cfd-build-base.dockerfile -t city4cfd-build-base --no-cache .

docker/city4cfd-build-base.dockerfile

@@ -0,0 +1,14 @@
+FROM ubuntu:jammy
+LABEL org.opencontainers.image.authors="Ivan Paden <[email protected]>"
+LABEL org.opencontainers.image.source="https://github.com/tudelft3d/city4cfd"
+LABEL org.opencontainers.image.vendor="Tudelft3D"
+LABEL org.opencontainers.image.title="City4CFD build base"
+LABEL org.opencontainers.image.description="Base image for building City4CFD"
+LABEL org.opencontainers.image.licenses="GPL-3.0"
+LABEL org.opencontainers.image.url="https://github.com/tudelft3d/city4cfd"
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    build-essential    \
+    cmake              \
+    libboost-all-dev   \
+    libcgal-dev  

docker/city4cfd.dockerfile

@@ -0,0 +1,74 @@
+FROM tudelft3d/city4cfd:build-base AS builder
+
+ARG JOBS
+
+#
+# Install City4CFD
+#
+COPY . /tmp
+
+RUN cd /tmp && \
+    mkdir build && \
+    cd build && \
+    cmake \
+#        -DCGAL_DIR=/usr/local \
+#        -DCMAKE_BUILD_TYPE=Release \
+#        -DBoost_NO_BOOST_CMAKE=TRUE \
+#        -DBoost_NO_SYSTEM_PATHS=TRUE \
+#        -DBOOST_ROOT=/usr/local \
+        .. && \
+    make -j $JOBS && \
+    make install && \
+    cd ~ && \
+    rm -rf /tmp/* && \
+    rm -rf /user/local/man
+
+RUN city4cfd --version
+
+# removing unnecessary headers
+RUN rm -rf /usr/local/include
+
+RUN mkdir /data && \
+    chown 1001 /data && \
+    chgrp 0 /data && \
+    chmod g=u /data && \
+    chgrp 0 /etc/passwd && \
+    chmod g=u /etc/passwd
+
+#
+# Export the dependencies
+#
+RUN mkdir /export
+COPY docker/strip-docker-image-export /tmp
+RUN bash /tmp/strip-docker-image-export \
+    -v \
+    -d /export \
+    -f /bin/bash \
+    -f /usr/bin/awk \
+    -f /usr/bin/id \
+    -f /etc/passwd \
+    -f /bin/ls \
+    -f /data \
+    -f /usr/local/share/proj/proj.db \
+    -f /usr/local/bin/city4cfd
+
+#
+# Create City4CFD image
+#
+FROM scratch AS exe
+ARG VERSION
+LABEL org.opencontainers.image.authors="Ivan Paden <[email protected]>"
+LABEL org.opencontainers.image.source="https://github.com/tudelft3d/city4cfd"
+LABEL org.opencontainers.image.vendor="Tudelft3D"
+LABEL org.opencontainers.image.title="City4CFD"
+LABEL org.opencontainers.image.description="City4CFD image"
+LABEL org.opencontainers.image.licenses="GPL-3.0"
+LABEL org.opencontainers.image.url="https://github.com/tudelft3d/city4cfd"
+LABEL org.opencontainers.image.version=$VERSION
+
+COPY --from=builder /export/ /
+
+WORKDIR /data
+
+ENTRYPOINT ["city4cfd"]
+CMD ["--help"]

docker/docker-compose.yml

@@ -0,0 +1,9 @@
+# docker-compose.yml
+
+version: '3.6'    
+services:
+  city4cfd:
+    build:
+      context: ../
+      dockerfile: ./docker/city4cfd.dockerfile
+    image: tudelft3d/city4cfd:test-container

docker/run/city4cfd_docker.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+docker run --rm -v 'pwd':/data tudelft3d/city4cfd:latest $@

docker/run/windows_city4cfd_run.bat

@@ -0,0 +1 @@
+docker run --rm -v %cd%:/data tudelft3d/city4cfd:latest %*

docker/run/windows_city4cfd_run.ps1

@@ -0,0 +1 @@
+docker run --rm -v "${pwd}:/data" tudelft3d/city4cfd:latest $args